Emperor
=======

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Emperor is a next-generation tool for the analysis and visualization of large microbial ecology datasets. Amongst its many features, Emperor provides a modern user interface that can be rapidly adjusted to your data analysis workflow.

To start using Emperor, please refer to the [installation notes](INSTALL.md).

Before contributing code to Emperor, please familiarize yourself with the [contributing guidelines](CONTRIBUTING.md).

## Usage

You can start using Emperor through [QIIME 2](https://qiime2.org)'s [interfaces](https://docs.qiime2.org/2021.2/interfaces/) (the command line or the graphical user interface), or alternatively using the Python interface (compatible with the Jupyter notebook, see [this example](http://nbviewer.jupyter.org/github/biocore/emperor/blob/new-api/examples/keyboard.ipynb)). For more details, refer to our [online documentation](http://emperor.microbio.me).

## Publications

- [EMPeror: a tool for visualizing high-throughput microbial community data](https://www.ncbi.nlm.nih.gov/pubmed/24280061). GigaScience, 2013.

- [Bringing the Dynamic Microbiome to Life with Animations](https://www.ncbi.nlm.nih.gov/pubmed/28081445). Cell Host & Microbe, 2016.